successfully installed, but no import?

[calico2019]

Hello, I cloned the directory from github, and then installed as directed. The installation seemed to be successful.

However when I open the notebook in jupyter lab, it says no module named wishbone.

Any suggestions?

[ManuSetty]

Hello - which version of python are you using? Can you try with Python 3.7?

[calico2019]

Hi Manu, Thanks for responding. I'm using python 3.7.1. I've tried on both my macbookpro local host as well as on a linux high performance cluster to which I have access. I seem to run into the same issue on both. [image: image.png] [image: image.png] After I clone the github file, I change directories into the wishbone folder and 'sudo pip3 install .' It returns saying that the install was successful, and at that point I open jupyter lab from the command line, open the notebook, run the first cell, and hit the 'no module named wishbone' error. Typically, I use 'conda install' to make sure my dependencies are all correct, but here I've followed your instructions and used pip3. Could that be contributing to this issue? Let me know if there is other information I can provide. Thanks, Linda

…

On Wed, Jul 3, 2019 at 6:55 PM Manu Setty ***@***.***> wrote: Hello - which version of python are you using? Can you try with Python 3.7? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69?email_source=notifications&email_token=AMPYJYGAR2EUZ7WUJU3WE2LP5VKBRA5CNFSM4H5HYCMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZGC73Y#issuecomment-508309487>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMPYJYCCNXGEUC3YXCVH2U3P5VKBRANCNFSM4H5HYCMA> .

[ManuSetty]

Is it possible that your pip3 is pointing to a different python installation compared to ipython/jupyter notebook.

You can definitely try conda install ..... or

You can activate your correct conda environment using
conda activate <env_name>
and then install using
pip install .....

[calico2019]

Hi Manu, How would I confirm if my pip3 is pointing to a different python installation than my ipython/jupyter notebook? When I look at the versions, I see pointing to anaconda's 3.7, so it should be correct right? If this is incorrect, please let me know how to change it. [image: image.png] Yes, I have tried both 'conda install .' and 'pip install .' and both throw errors on my macbook pro and on my linux machine (see below). Neither MBP or linux can use conda to install the package because it's not a tarball format. [image: image.png] MBP also fails on pip install . [image: image.png] linux HPC: similar error, but on gsea. [image: image.png] Please let me know if there is anything else I can try--Per Smita Krishnaswamy's suggestion, I'd really like use wishbone with my mass cytometry data. Thanks again for your help, Linda

…

On Thu, Jul 4, 2019 at 5:30 AM Manu Setty ***@***.***> wrote: Is it possible that your pip3 is pointing to a different python installation compared to ipython/jupyter notebook. You can definitely try conda install ..... or You can activate your correct conda environment using conda activate <env_name> and then install using pip install ..... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#69?email_source=notifications&email_token=AMPYJYHZ4A3WQNZMBM6AP7DP5XUNHA5CNFSM4H5HYCMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZHJCEI#issuecomment-508465425>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMPYJYA2N3LNT4YMLDNMYHLP5XUNHANCNFSM4H5HYCMA> .

[ManuSetty]

Hi Linda

Yes, the way you are checking makes sense. The images of error did not come through - can you please send them again.

[calico2019]

Resending previous email with new images pasted: Hi Manu, How would I confirm if my pip3 is pointing to a different python installation than my ipython/jupyter notebook? When I look at the versions, I see pointing to anaconda's 3.7, so it should be correct right? If this is incorrect, please let me know how to change it. [image: image.png] Yes, I have tried both 'conda install .' and 'pip install .' and both throw errors on my macbook pro and on my linux machine (see below). Neither MBP or linux can use conda to install the package because it's not a tarball format. [image: image.png] MBP also fails on pip install . [image: image.png] linux HPC: similar error, but on gsea. [image: image.png] Please let me know if there is anything else I can try--Per Smita Krishnaswamy's suggestion, I'd really like use wishbone with my mass cytometry data. Thanks again for your help, Linda

…

On Thu, Jul 4, 2019 at 11:30 AM Linda Fong ***@***.***> wrote: Hi Manu, How would I confirm if my pip3 is pointing to a different python installation than my ipython/jupyter notebook? When I look at the versions, I see pointing to anaconda's 3.7, so it should be correct right? If this is incorrect, please let me know how to change it. [image: image.png] Yes, I have tried both 'conda install .' and 'pip install .' and both throw errors on my macbook pro and on my linux machine (see below). Neither MBP or linux can use conda to install the package because it's not a tarball format. [image: image.png] MBP also fails on pip install . [image: image.png] linux HPC: similar error, but on gsea. [image: image.png] Please let me know if there is anything else I can try--Per Smita Krishnaswamy's suggestion, I'd really like use wishbone with my mass cytometry data. Thanks again for your help, Linda On Thu, Jul 4, 2019 at 5:30 AM Manu Setty ***@***.***> wrote: > Is it possible that your pip3 is pointing to a different python > installation compared to ipython/jupyter notebook. > > You can definitely try conda install ..... or > > You can activate your correct conda environment using > conda activate <env_name> > and then install using > pip install ..... > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#69?email_source=notifications&email_token=AMPYJYHZ4A3WQNZMBM6AP7DP5XUNHA5CNFSM4H5HYCMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZHJCEI#issuecomment-508465425>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AMPYJYA2N3LNT4YMLDNMYHLP5XUNHANCNFSM4H5HYCMA> > . >

[calico2019]

Hi Manu, I have also sent the .png files in case the first resend try didn't work. I apologize for sending the images one at a time, it seems like they are too large to be sent to the github email all at once. I really appreciate you taking the time to help me! Thanks again, Linda

…

On Thu, Jul 4, 2019 at 3:31 PM Linda Fong ***@***.***> wrote: On Thu, Jul 4, 2019 at 3:31 PM Linda Fong ***@***.***> wrote: > > > On Thu, Jul 4, 2019 at 3:30 PM Linda Fong ***@***.***> wrote: > >> >> >> On Thu, Jul 4, 2019 at 3:30 PM Linda Fong ***@***.***> wrote: >> >>> >>> >>> On Thu, Jul 4, 2019 at 1:28 PM Manu Setty ***@***.***> >>> wrote: >>> >>>> Hi Linda >>>> >>>> Yes, the way you are checking makes sense. The images of error did not >>>> come through - can you please send them again. >>>> >>>> — >>>> You are receiving this because you authored the thread. >>>> Reply to this email directly, view it on GitHub >>>> <#69?email_source=notifications&email_token=AMPYJYCV5BAFOX4FD2JQBPTP5ZMOHA5CNFSM4H5HYCMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZIC3HY#issuecomment-508571039>, >>>> or mute the thread >>>> <https://github.com/notifications/unsubscribe-auth/AMPYJYFF3E4H2U3JK7NIQ2TP5ZMOHANCNFSM4H5HYCMA> >>>> . >>>> >>>

[ManuSetty]

Sorry - the images are not coming through for some reason. Can you please email me directly at manu.talanki AT gmail.com

In the meantime, you can also have a look at our algorithm Palantir. Palantir generalizes to beyond two branches and also provides information about continuities in cell fate choices.
https://github.com/dpeerlab/palantir